Can we use JR Pass 7 days from Shinjuku to Odawara?Yes. Either by Yamanote Line and Tokaido Shinkansen via Shinagawa or by direct Shonan-Shinjuku Line.
I read that it is only Nozomi train available.
No, to the opposite! The nozomi is one of the only JR train that is NOT covered by the Japan Rail Pass.
Also is it cheaper to buy Hakone FreePass if i want to go to Kyoto straight from Hakone?
If you have a Japan Rail Pass, you should buy the Hakone Rail Pass at Odawara Station for use from Odawara Station.
Even if you don't have a Japan and visit Hakone along the way from Tokyo to Kyoto, buy a Hakone Rail Pass, which does not include the round trio from/to Tokyo.